ArticleBioinformatics (Oxford, England)2020
Detecting and correcting misclassified sequences in the large-scale public databases.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.Nature biotechnology · 2026Article
- Genomic insights intoMicrobiology spectrum · 2026Article
- Artificial intelligence-powered microscopy: Transforming the landscape of parasitology.Journal of microscopy · 2026Review
- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.bioRxiv : the preprint server for biology · 2025Article
- Article
- An Epidemic of Respiratory and Ocular Infections Caused by the Reemergence of a Recombinant Human Adenovirus, the Novel Type HAdV-B114 (P7H3F3).Journal of medical virology · 2025Article
- DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes.BMC bioinformatics · 2025Article
- Clarifying species boundaries between bocachico (Frontiers in genetics · 2025Article
- Direct On-Chip Diagnostics ofBiomolecules · 2024Article
- Disentangling cobionts and contamination in long-read genomic data using sequence composition.G3 (Bethesda, Md.) · 2024Article
- BakRep - a searchable large-scale web repository for bacterial genomes, characterizations and metadata.Microbial genomics · 2024Article
- The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals.Database : the journal of biological databases and curation · 2024Article
- In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences.PLoS computational biology · 2024Article
- Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.Nature communications · 2024Article
- Transcriptome of the pygmy grasshopperPeerJ · 2023Article
- Ten simple rules for investigating (meta)genomic data from environmental ecosystems.PLoS computational biology · 2022Article
- Propagation, detection and correction of errors using the sequence database network.Briefings in bioinformatics · 2022Review
- A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications.GigaScience · 2022Article
- Article
- Concatenated 16S rRNA sequence analysis improves bacterial taxonomy.F1000Research · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAs the cost of sequencing decreases, the amount of data being deposited into public repositories is increasing rapidly. Public databases rely on the user to provide metadata for each submission that is prone to user error. Unfortunately, most public databases, such as non-redundant (NR), rely on user input and do not have methods for identifying errors in the provided metadata, leading to the potential for error propagation. Previous research on a small subset of the NR database analyzed misclassification based on sequence similarity. To the best of our knowledge, the amount of misclassification in the entire database has not been quantified. We propose a heuristic method to detect potentially misclassified taxonomic assignments in the NR database. We applied a curation technique and quality control to find the most probable taxonomic assignment. Our method incorporates provenance and frequency of each annotation from manually and computationally created databases and clustering information at 95% similarity.
resultsWe found more than two million potentially taxonomically misclassified proteins in the NR database. Using simulated data, we show a high precision of 97% and a recall of 87% for detecting taxonomically misclassified proteins. The proposed approach and findings could also be applied to other databases. AVAILABILITY AND IMPLEMENTATION: Source code, dataset, documentation, Jupyter notebooks and Docker container are available at https://github.com/boalang/nr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.